6S16

T. thermophilus RuvC in complex with Holliday junction substrate

Summary for 6S16

• Entry DOI: 10.2210/pdb6s16/pdb
• Descriptor: Crossover junction endodeoxyribonuclease RuvC, DNA (33-MER), DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3'), ... (6 entities in total)
• Functional Keywords: ruvc resolvase holliday junction, hydrolase
• Biological source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); More
• Total number of polymer chains: 5
• Total formula weight: 66616.24

Authors

Gorecka, K.M.,Krepl, M.,Szlachcic, A.,Poznanski, J.,Sponer, J.,Nowotny, M. (deposition date: 2019-06-18, release date: 2019-09-25, Last modification date: 2024-01-24)

Primary citation

Gorecka, K.M.,Krepl, M.,Szlachcic, A.,Poznanski, J.,Sponer, J.,Nowotny, M.
RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution.
Nat Commun, 10:4102-4102, 2019

PubMed Abstract: Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution of the HJ, the two cuts need to be tightly coordinated. They are also specific for cognate DNA sequences. Using a combination of structural biology, biochemistry, and a computational approach, here we show that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA. These changes involve rare high-energy states with protein-assisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences. These conformational changes and the relief of protein-induced structural tension of the DNA facilitate coordination between the two cuts. The unique DNA cleavage mechanism of RuvC demonstrates the importance of high-energy conformational states in nucleic acid readouts.

PubMed: 31506434
DOI: 10.1038/s41467-019-11900-8

Experimental method

X-RAY DIFFRACTION (3.409 Å)